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Recent Activity
Debbie Jacobs-Sera posted in anti-CBASS type III-C protein
Debbie Jacobs-Sera posted in F1 cluster forward reverse or neither?
Allison Johnson posted in anti-CBASS type III-C protein
c.sunnen posted in F1 cluster forward reverse or neither?
Debbie Jacobs-Sera posted in F1 cluster forward reverse or neither?
All posts created by aajohnson
Link to this post | posted 06 May, 2024 19:37 | |
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Hi! This is an investigation of function for Balomoji protein #102 (Pecaan) or 102 (final DNAMaster file), genome coordinates 60991-61688, pham 163488. We answer the required questions and make a pitch in this google doc for consideration of function related to cyclic trinucleotide binding anti-CBASS proteins, inspired by Dr. Bondy-Denomy's SEA Symposium presentation. Allison and two fantastic students who did this work, Harshini and Mariya |
Link to this post | posted 12 Apr, 2023 19:57 | |
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Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). Allison |
Link to this post | posted 12 Apr, 2023 19:57 | |
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Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ |
Link to this post | posted 12 Apr, 2023 19:57 | |
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Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ |
Link to this post | posted 12 Apr, 2023 19:57 | |
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Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ |
Link to this post | posted 05 Apr, 2023 18:40 | |
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We are trying to figure out how/why the major tail protein (LittleFortune gene 31, pham 74364, sequence file attached) is annotated with this function in Microbacteriophages. There is no functional annotation evidence support through blastp CDD or HHPred. The Microbacteriophages paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636) describes the major tail protein twice, such as "and the major tail protein gene is atypically located upstream of some of the head-to-tail connector genes". Some maps have this label on a protein, we just can't figure out where this label is coming from. Point me in the right direction please? |
Link to this post | posted 23 Feb, 2023 13:40 | |
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Perfect, thank you. |
Link to this post | posted 22 Feb, 2023 20:25 | |
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This was useful today! Thank you. |
Link to this post | posted 22 Feb, 2023 20:00 | |
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debbie |
Link to this post | posted 04 Feb, 2016 18:52 | |
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I'm definitely interested. My student work on laptops, and we create a Windows VM for the students with Macs to run DNA Master but it's a hassle for a variety of reasons. I'd love it they only had one install. |